Abstract
Within the last few years, there have been an increased number of clinical studies involving urinary microbiota. Low-biomass microbiome sequencing (e.g., urine, lung, placenta, blood) is easily biased by contamination or cross-contamination. So far, a few critical steps, from sampling urine to processing and analyzing, have been described (e.g., urine collection modality, sample volume size, snap freezing, negative controls usage, laboratory risks for contamination assessment, contamination of negative results reporting, exploration and discussion of the impact of contamination for the final results, etc.) We performed a literature search (Pubmed, Scopus and Embase) and reviewed the published articles related to urinary microbiome, evaluating how the aforementioned critical steps to obtain unbiased, reliable results have been taken or have been reported. We identified different urinary microbiome evaluation protocols, with non-homogenous reporting systems, which can make gathering results into consistent data for similar topics difficult and further burden the already so complex emerging field of urinary microbiome. We concluded that to ease the progress in this field, a joint approach from researchers, authors and publishers would be necessary in order to create mandatory reporting systems which would allow to recognize pitfalls and avoid compromising a promising field of research.
Highlights
IntroductionThe urinary tract was considered a sterile environment until the last decade when high throughput molecular DNA sequencing technologies demonstrated the contrary: even in the absence of urinary tract infection, the urine is not a sterile biofluid; it contains a variable microbial spectrum and the Diagnostics 2020, 10, 343; doi:10.3390/diagnostics10060343 www.mdpi.com/journal/diagnosticsDiagnostics 2020, 10, 343 imbalance of the urinary microbiome is supposed to be involved in different urologic pathologies [1,2,3].In-depth knowledge of urinary microbiota is expected to offer a better understanding of its metabolic, functional and networking aspects, to unveil the pathogenic pathways in urologic diseases and to further guide specific treatments [1].The perspective of urinary microbiome as the “magic bullet” for the good health status of the urinary system and the opportunity to find correlations or to fathom its role in disease mechanisms led to a rapid shift in the number of studies aiming to identify urinary microbiome’s classes, orders, families, genera and even distinct species
We reviewed how the essential steps of microbiome analysis methodology—described so far in the literature as prone to potential risks, controversies and pitfalls related to contamination and bias risks—have been implemented in order to avoid the potential biases within clinical studies as a prerequisite to fully relying on further microbiome-related answers to clinical questions
Articles in other languages than English, articles without an abstract, those without original data, or not evaluating human urinary microbiota, those without a detailed description of the technique/study method and those using techniques other than 16S rRNA PCR amplification of the bacterial DNA were excluded from the final analysis
Summary
The urinary tract was considered a sterile environment until the last decade when high throughput molecular DNA sequencing technologies demonstrated the contrary: even in the absence of urinary tract infection, the urine is not a sterile biofluid; it contains a variable microbial spectrum and the Diagnostics 2020, 10, 343; doi:10.3390/diagnostics10060343 www.mdpi.com/journal/diagnosticsDiagnostics 2020, 10, 343 imbalance of the urinary microbiome is supposed to be involved in different urologic pathologies [1,2,3].In-depth knowledge of urinary microbiota is expected to offer a better understanding of its metabolic, functional and networking aspects, to unveil the pathogenic pathways in urologic diseases and to further guide specific treatments [1].The perspective of urinary microbiome as the “magic bullet” for the good health status of the urinary system and the opportunity to find correlations or to fathom its role in disease mechanisms led to a rapid shift in the number of studies aiming to identify urinary microbiome’s classes, orders, families, genera and even distinct species. Studies involving microbiome have tried to find correlations with cancer, diabetes, autism, urinary stone disease, prostate cancer, bladder cancer, etc. Hanage mentioned, this emerging field—the microbiome—should be extremely meticulously and cautiously explored, being of paramount importance to unveil at least a few aspects: whether the current experiments detect differences that matter, to find the differences between causation and correlation and to find the mechanisms of action. This emerging field—the microbiome—should be extremely meticulously and cautiously explored, being of paramount importance to unveil at least a few aspects: whether the current experiments detect differences that matter, to find the differences between causation and correlation and to find the mechanisms of action He suggested to look dispassionately at the data. As “in pre-scientific times when something happened that people did not understand, they blamed spirits”, nowadays “we must resist the urge to transform our microbial passengers into modern-day phantoms” [4]
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